5MRH

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1

• PDB DOI: https://doi.org/10.2210/pdb5MRH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-12-23 Released: 2017-05-17 
• Deposition Author(s): Andersen, J.L., Strandbygaard, D., Thirup, S.
• Funding Organization(s): DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron Facilities, Biostruct-X

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.95 kDa 
• Atom Count: 5,157 
• Modelled Residue Count: 639 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A	696	Homo sapiens	Mutation(s): 0  Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens) Explore Q99523  Go to UniProtKB:  Q99523
PHAROS:  Q99523 GTEx:  ENSG00000134243

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q9Z	D [auth A]	3-(3-methylbutyl)-4~{H}-1,2,3-triazol-5-one C7 H13 N3 O NRFSJPLMHMLGTM-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q9Z	BindingDB:  5MRH	IC50: 6.31e+4 (nM) from 1 assay(s)
	Binding MOAD:  5MRH	IC50: 6.31e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.395	α = 90
b = 78.23	β = 127.2
c = 111.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Andersen, J.L., Strandbygaard, D., Thirup, S.

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Funding Organization	Location	Grant Number
DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron Facilities	Denmark	--
Biostruct-X	Denmark	283570

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary